Chuck Vs the Rose Thorn
by jojobevco
Summary: When Ellie starts getting suspicious of Sarah Walker, she'll take action. Action that will bring her past into the the open. A past that she kept secret for very important reasons. A past that will change Chuck, Fulcrum and the US Government.
1. Contemplations of a Doctor

Disclaimer: I do not own the rights to the _Chuck_ TV series or characters. I do, however, reserve the rights for any characters I develop and the plot of this story.

Chuck vs. the Rose Thorn

By Jojobevco

Chapter 1

Contemplations of a Doctor

AN: Welcome to my latest project, Chuck vs. the Rose Thorn. This story came into my head one night while watching repeats of Chuck and after reading stories like Chuck Vs. the Scarlet Ibis. I finally decided to write it after reading some comments by Josh Schwartz (one of the show creators) about their initial plans to turn Captain Awesome into an enemy spy at the end of season one.

This story takes place after "Chuck Versus the Ring."

Dr. Eleanor Fay Woodcomb (nee Bartwoski) was sitting in the Orange Orange enjoying her small vanilla yogurt. While Ellie believed in eating healthy, she also believed that it was good to treat yourself once in a while. Sarah Walker, her brother's girlfriend, was walking around behind the counter.

Ellie had to say she was happy that Sarah came into Chuck's life. She was the person to really pull Chuck out of the funk he had been in for years after the whole Bryce and Jill thing; something Ellie still felt bad about. Chuck was a good guy. She was sorry to see that sort of terrible thing happen to him.

Ellie continued watching Sarah as she moved around behind the counter. Ellie always felt there was something off about Sarah; something just didn't sit right with her about it. The way Sarah acted it seemed familiar, it almost reminded Ellie of herself. Of course, that's absolutely preposterous, what would a frozen yogurt girl have in common with a trauma surgeon? However, the comparison her subconscious was making unsettled her.

Then Sarah's phone started ringing, the young blond answered it.

"Walker, yes, okay, I'll be right there." Sarah hung up.

"Sorry, Ellie, I have to close up early today, emergency meeting at corporate."

"Oh, uh okay."

While Ellie was happy to have Sarah in her brother's life, Ellie didn't completely trust her. First, the whole way they met was suspicious. While her brother was a good person and one she hoped would find happiness in his sad life, frankly there was no way he could attract a woman like Sarah. Then, there were all the strange mugging and other accidents that Chuck and Sarah had. Oh, and most importantly there was the Porsche that Sarah, a food service industry employee, drives.

Today, however, Ellie was really suspicious. How the hell could a yogurt company have an emergency? Ellie quickly said good-bye to Sarah and walked out and went to her car outside the parking lot. It was time to get some answers. Ellie drove away from the store to the other side of the parking lot. She lowered her window and pulled a pair of binoculars out of the center console that she kept for bird watching. Ellie had always loved bird watching. It was something she had picked up years ago, when she did a two year stint with Doctors Without Borders in Africa, after which, she had reconnected with Devon.

Ellie sighed in delight after thinking of Devon. Devon Woodcomb was truly was the love of her life, after all those years, all those bodies, all that blood, to be able to come home to him, it reminded her that there was good in the world.

She saw Sarah walk into the freezer and not come out. She waited and waited. Finally, Sarah came out of the freezer, but she wasn't alone. Their neighbor, John Casey was there with her. He was holding something. Ellie zoomed in. It was a gun, a Sig Saur P229, to be exact. John stood around for a while before leaving and walking across the street into the Buy More.

Sarah had said that she had not been around guns during Christmas and that whole terrible hostage situation, yet here was a man with a gun and she didn't seem fazed by it. Eventually, she decided to confront her "best friend" about it. She grabbed a few things out of her car and walked back toward the store. She opened the door and walked in.

"Ellie, long time, no see," Sarah joked.

Ellie kept smiling, "Hello, Sarah how was the meeting at corporate."

"Oh, the usual, not enough demand too much production."

"Really, and does corporate happen to be in your freezer?"

Sarah was confused, did Ellie know something, or was she making a joke.

"What, Ellie?"

"I know you were in your freezer the whole time and I know John Casey was in there with you."

"Ellie, it's not what it looks like; I'm not cheating on Chuck, especially with John Casey." Sarah laughed at the absurdity of the situation.

"No, it wasn't that he was in there, it was more the Sig P229 that he had on him I thought you didn't like guns Sarah?"

Ellie then reached behind her and pulled out her Heckler and Koch P2000 sub-compact, loaded with 12 .40 Smith &Wesson rounds.

"Why don't you tell me exactly what's going on, Sarah, hmm?"

AN: And cue the running Nerd Herd guy. Please Review. If there is sufficient interest I'll continue it.


	2. Agent Rose Thorn

Disclaimer: I do not own the rights to the _Chuck_ TV series or characters. I do, however, reserve the rights for any characters I develop and the plot of this story.

AN: In response to several negative reviews about the believability of Ellie's character and some misunderstandings, I have decided to revise and repost this chapter.

Chuck vs. the Rose Thorn

By Jojobevco

Chapter 2

Agent Rose Thorn

For the first time in her life, Sarah Walker was shocked beyond all possible comprehension. Was _Ellie Woodcomb_ a member of Fulcrum or worse, The Ring?

"Ellie, why don't you put the gun down and we can talk about this."

"No, I'm not putting my gun down. Now tell me, why were you in the freezer for thirty minutes and why you walked out with John Casey, oh and while we're on it, why did John Casey have a gun?"

"Ellie, I can't tell you that."

"Oh, yes you can, otherwise it's a bullet in your skull. Now what are you doing here and how is my brother involved?"

Sarah sighed, "Ellie, I work for the CIA, Casey's a member of the NSA; we're here to protect Chuck."

"Why does Chuck need protection?"

"I can't tell you that Ellie."

"Of course, national security crap I guess? Can prove you are CIA? Because right now, I'm leaning toward drug dealer, or terrorist, more drug dealer because of the car." After all most terrorists don't drive a Porsche.

"Yes, I'll take you down stairs."

"Nope, not going anywhere, call who you need to, Sarah, but we're not leaving."

Sarah slowly reached for her cell phone, pulled it out and dialed Beckman.

"Put it on speakerphone."

_"Beckman, Secure."_

"Walker, Secure. General, we have a problem here."

_"What sort of problem?"_

"Ellie Woodcomb has a gun pointed at my head."

_"Back it up, Ellie Woodcomb? Seriously, the girl is actually holding a gun to your head?"_

"Uh, yes ma'am."

"Can we get back to who are you talking to?"

_"Doctor Woodcomb, I'm General Louisa Beckman, NSA, now why exactly are you pointing a gun at Agent Walker's head?"_

"How do I know you really are NSA, and not something like Fulcrum?"

_"How do you know about Fulcrum, Doctor?"_

"Oh, I know Fulcrum very well; I was on their tail for almost five years."

Of course, this was the exact moment Chuck had to walk into Orange Orange, "Hey Sarah, um," Chuck looked up to his phone to see his sister pointing a gun at Sarah's head, "what's going on?"

"Chuck, I want you to go and stand over there," she used her free hand to point to an area off to the side of the store away from her and Sarah.

"Ellie?" Why did his innocent and sweet sister have a gun?

"Now, Chuck!"

Ellie turned back to the iPhone, "What were you saying, General?"

_"You were with the Agency?"_

"For about five years from 2001 to 2005. My Codename was… "

For some odd reason Chuck started muttering, "Don't say it, don't say it."

"…Rose Thorn."

Chucks eyes started Fluttering. He was Flashing.

_Picture of a Rose_

_Ellie's Dossier_

_Ellie's Medical Degree_

_Ellie's Censored Dossier_

_Ellie Shooting a Fulcrum Agent_

_Ellie Shooting another Fulcrum Agent_

_Ellie Shooting yet another Fulcrum Agent_

_Operation Counterweight_

_Ellie's Discharge Papers_

_Order for Purging Ellie's Records_

_Picture of a Rose_

"Eleanor Fay Bartowski, Codename Rose Thorn, former CIA agent that killed or captured over 80 Fulcrum agents over a five year period. Directed Operation Counterweight for four years before retiring in 2005 for personal and security reasons, and had her records purged," after the flash Chuck blinked for a few minutes, "so those two years in Doctors without Borders?"

"I was never involved in it. Devon and I met on the flight back to LA from Washington. He doesn't know that I never actually was in Africa. Wait, how the hell did you become the Intersect? I thought I took care of that when I had Bryce expel you from Stanford."

"Wait, you had Bryce expel me?"

"Well, he didn't know it was me that told him. I would rather have you depressed than dead and trust me; you were closer to dead than you think. So Sarah really is your CIA handler?"

"Yeah."

"Oh, okay," Ellie holstered her gun, "Now could someone explain to me why you're still fighting Fulcrum four years after I left."

_ "Fulcrum is a very dangerous organization. You have no idea how dangerous they are. They've grown significantly since you left."_

"Actually, General, I probably have a very good idea about the dangers of Fulcrum; Operation Counterweight was responsible for investigating and eliminating the Fulcrum elements inside the US Government. We were very good at our jobs. In fact, Fulcrum was on its death bed before I left. What I want to know, General, is why Fulcrum was allowed to resurface?"

_"We should discuss this in a more secure location Dr. Woodcomb."_

"It's Agent Bartowski now, General."

_"We will discuss that later on. Agent Walker, please escort Dr. Woodcomb and her brother down to Castle." _The iPhone clicked off.

"It's Agent Bartowski, you bitch."

"Ellie!"

"What? I hate bureaucrats. Bitchman is right about one thing, we should discuss this in a more secure location. So, Sarah, I'm guessing your Castle is in your freezer."

"Um, yes."

"Then lead on."

Five minutes later saw Sarah, Ellie, Chuck, and Casey, who had been called back over from the Buy More, sitting around Castle's conference table. Ellie was telling her story.

"I was recruited right after Med School. Originally I was a Medical Officer/Analyst at Langley, you know stare at a picture of some guy and figure out what's wrong with him. Rather boring. Chuck, you were starting college at the time, so I knew you wouldn't miss me that much."

Chuck nodded; he had spent a lot of time doing study abroad and internships during his summer months.

"The Medical Officer idea lasted all of a month before my file happened to cross the desk of Langston Graham. He determined that my talents were being 'wasted' and had me shipped to The Farm. Apparently, I was very good at subliminal image processing," she glanced at Chuck, "must run in the family, I suppose."

"A few months later, I was a full-fledged CIA agent. The mission I was given was rather simple, on paper. I was ordered to investigate and hunt down members of a rogue organization know as," She waved her hand to the three of them, "well don't everyone chime in at once."

"Fulcrum," Chuck and Sara droned, Casey merely grunted.

"Yep, it was hard to say the least, here I was, a new agent against some of the best in the industry."

"Why would Graham trust you with the mission then?"

"The intelligence community was more compromised then you think. The chain of command for my mission was rather simple, because there were only three people we knew were not Fulcrum, Me, Graham, and the President. Langston Graham, no offense intended, Sarah, couldn't trust anyone more senior than me because he wasn't sure who was Fulcrum and who wasn't, they were everywhere, in the corner of every greedy power hungry bureaucrat in Washington. He needed a new face, an unknown factor to go after them. He, damn him for it, picked me."

"So how did Operation Counterweight come about?"

"Eventually, we realized that I was just taking out the edges, small fish, and occasionally cells when Fulcrum slipped up. We also realized that our efforts were being blocked on some of the highest levels."

"What do you mean?"

"We uncovered that two agency deputy directors and one agency director were Fulcrum. We ended up forming an inter agency task force, the whole alphabet soup."

"Operation Counterweight."

"Exactly, we started pooling and sharing resources, we found patterns we even managed to get a mole inside Fulcrum, who was very close to the leadership. We were the only ones in the Government that could be trusted. We answered to only the President."

"How many of you were there?"

"There were ten of us."

Casey was a bit suspicious of this, "How did the ten of you manage to check a few million government employees by yourselves?"

"Simple, we used the Intersect. Originally the Intersect was designed to be run out of a computer lab or downloaded into someone's head. Each option has its pros and cons. The computer lab gives us a searchable index. In a few seconds we can cross-reference the collective knowledge of the US Government. The download creates a mobile unit, suitable for field work."

"Why did you leave?"

"I was burning out fast. I had not seen Chuck for two years. We were closing in on Fulcrum, we had them cornered, and then my cover almost got blown. I still don't know how that happened. That was when I realized I had to leave. If they found out who Rose Thorn was, then Chuck would be in danger. That was why I ordered Bryce to have you expelled from Stanford; I didn't want this life for you. Hell, I didn't want it for me. After my cover was almost blown I had to leave. I submitted my resignation, ordered my records purged and caught a flight back to LA, where I reconnected with Devon."

"And the rest is history."

"Exactly, Chuck. Now what I want to know is what happened after I left?"

_"We don't know, Agent Bartowski."_

"What do you mean General Beckman?"

_"Apparently along with your records, the entire operation was purged from our records, we have no idea what happened after you left. The only other people we know were involved were Graham and Larkin, both of whom are now dead."_

"Well then I might know someone who knew what happened. I might even know their whereabouts. I recently found out that my mole inside Fulcrum has resurfaced."

_"Who is this mole?"_

"Chuck, when was the last time you saw Jill Roberts?"

AN: Please review, thanks to those who have.


	3. A Variety of Conversations

Disclaimer: I do not own the rights to the _Chuck_ TV series or characters. I do, however, reserve the rights for any characters I develop and the plot of this story.

Chuck vs. the Rose Thorn

By Jojobevco

Chapter 3

A Variety of Conversations

"Um, what?"

"You know Jill Roberts, your ex-girlfriend, the woman you think of as evil incarnate?"

"Oh, _that_ Jill Roberts, um, I don't know."

"What do you mean you don't know? I know she was in town recently, you yourself told me as much."

Casey chipped in an explanation, "Moron here let her escape."

"I was just keeping up our end of a bargain."

"My brother is not a moron, John, although he is thankfully not as coldhearted as you, no offense intended."

Casey grunted.

_"Jill Roberts, the woman who helped Fulcrum infiltrate Castle and tried to kill most of my agents, including Chuck, on more than one occasion is your mole?"_

"Yes, she is. I presume that after she lost contact with Counterweight, she went off mission, simply integrating herself with Fulcrum. Her code name was," she turned to face Chuck, "Seashore."

The intersect in Chuck's head, combining what he knew about Jill, flashed. Everyone in the room patently wait for his eyes to stop shaking.

"She's right, Jill was a CIA planted mole inside Fulcrum, her college life shaped her for recruitment by Fulcrum. She was a loyal CIA agent, until the records suddenly cut off in 2005."

Ellie nodded, "When I left."

Casey grunted, "Higher ups probably burned her."

_"Very well, for the time being, I will rescind the kill order on Jill Roberts. We'll try to contact her. I'll update you later. Beckman out." _The screen went back to the NSA logo.

"Hmm, well we could do that, Bitchman, or I could just call her." Ellie went to the desk and picked up a phone before dialing a number. The phone rang and then one of those annoying as heck automated prompt machines answered.

_"Thank you for calling Fulcrum, Please enter your access code now."_

Ellie punched in a few numbers, and then the voice gave out a series of numbers, an IP address. Ellie walked over to a computer and entered the IP address before a series of codenames came up. Ellie clicked on "Sandstorm" Jill's Fulcrum codename and a message box came up. She sent the following message.

_Sandstorm/ J,_

_ Meet me and C at Casa B in Echo Park. Have explained your situation. Will brief you on arrival. _

_ RT/EFB_

She clicked send.

"Well, I hope that works."

"Wait, you know how to get into Fulcrum's contact protocols?"

"I have an old access code to the system. I guess they never changed it. Jill will be stopping by our house shortly. Chuck, John, head for the house. Sarah and I will follow in a moment." Chuck and Casey knew what a dismissal looks like, so they left.

"Agent Walker, what are your feelings toward my brother?"

Sarah sighed, why the hell was everyone asking her that, "Agent Bartowski, I can…"

"No, Sarah, I'm not talking to you as Rose Thorn. I'm talking to you as Chuck's Sister, so tell me the truth, are you feelings for Chuck a cover or are they real?"

Sarah sighed, more than before, "No, they're real."

"Well then you did a very good job of hiding them from the higher ups."

"Not exactly, I did get a 49b."

"Who did Beckman send?"

"Agent Alex Forrest."

"Forrest, I never liked her, she was on my team you know."

Sarah, smirked wait for it, wait for it.

"OH MY GOD! Was Forrest at Devon's Bachelor Party?"

"Yep that was her, besides she was an absolute bitch to Chuck, I wanted to kick her ass all the time."

"You're not the only one, let's go." Halfway up the stairs to the Orange Orange she stopped, "Actually, um, we have one more stop to make." Then she headed for the door to the Buy More.

The Buy More Break Room was empty, with the exception of one worker, Anna Wu. Ellie started reaching for the locker door release switch, before Sarah stopped her.

"What are you doing? If Anna sees us you'll blow our cover. "

"Just get down, alright; I know what I'm doing." She hit the release button and the door swung open. Instantly a knife went flying right where her head would have been. Said knife was quickly followed by a fork.

"Come out of there right now, or else I'll…I'll carve your heart out with a spoon!"

Ellie stepped up into the store, "Stand down, Anna."

"Ellie?"

"Something's come up. Let's just say, Fulcrum is not as dead as we thought. I've been reactivated. Do you want to join me? It's completely up to you."

"Yes, ma'am, I'm with you."

"I know that's what you would say, come on, I trying to arrange a meeting with Seashore."

"And her, ma'am?" Anna asked, gesturing to Sarah.

"Sarah is CIA."

"Well that explains a lot."

They walked out to the parking lot. Ellie went to her car, while Sarah and Anna went to Sarah's Porsche. As they were driving, Sarah tried to make conversation.

"How did you and Ellie meet?"

"I was one of the last additions to Operation Counterweight. At the time I was a liaison to the CIA from Taiwan's National Security Bureau. I was operating in the LA area, infiltrating a Triad with ties to Fulcrum. My cover was blown, I was captured, and you can imagine the rest I assume."

Sarah nodded; torture was rather common in their profession.

"Anyway they were about to kill me when Ellie's team burst in and rescued me while on an intel gathering op. She later said that she had no idea I was there. Apparently both the CIA and the NSB didn't think it worth their while to rescue me. She asked me to join her team, and I did as a full-fledged CIA agent. I owe Ellie my life, for that time and a quite a few after it. I would follow that woman anywhere. We were together when our covers almost got blown. Afterwards, I really had no place to go. I had to hide. Fulcrum knew I was ex-NSB, so I couldn't go back to Taiwan. Ellie set me up here in LA and the rest is history.

By this time, they had arrived at Casa Bartowski along with Ellie. They both got out and walked into the house. Chuck spotted them.

"Anna? What are you doing here?"

"Actually, I was about to ask you the same question, Chuck."

Ellie explained, "Anna, Chuck is the Intersect."

"Oh, well in that case you would probably know me better as Lilly Dao."

Chuck flashed. By the end of it, he looked a little annoyed.

"Oh, for crying out loud, is everyone I know a spy?"

"I get that feeling as well, Chuck."

Everyone spun around to look at Chuck's bedroom door, Sarah and Casey drew their guns. Ellie just smiled.

"Sorry, I used the Morgan Door. You rang, Ellie?"

Jill Roberts had arrived.

AN: Please Review, thanks to those who have.

AN2: I decided to make Anna a spy because I thought that at least one more person Chuck knew from his "real life" should be on Ellie's team. Remember her team consisted of ten people. I've already identified five of them: Ellie, Bryce, Jill, Alex Forrest, and Anna. Chuck will have previously met at least one more of the members (he met this member in the spy world, not his real life).

AN3: I'm trying to think about what sort of relationships Ellie would have had in her past. Any suggestions?


	4. Disagreements and Explanations

Disclaimer: I do not own the rights to the _Chuck_ TV series or characters. I do, however, reserve the rights for any characters I develop and the plot of this story.

Chuck vs. the Rose Thorn

By Jojobevco

Chapter 4

Disagreements and Explanations

AN: Well, after having seen the premiere for Chuck I have to say I am not happy with the producers. They've made the show so, not Awesome. First, the "Prague Debacle" which I think really would not have happened; Chuck would have been on a train and had the government on his tail. Oh and how dare they get rid of Anna! Also, the opening scene from "Chuck vs. the Angel of Death" reveals that Ellie and Awesome started medical school in 2000. **Anyway what this means for my story, is that it is going AU from the first week after the events of Chuck vs. the Ring, before Morgan and Anna pack it up for Hawaii, and before Chuck decides to leave for Prague. Furthermore, Elle graduated medical school in 2001.**

AN2: On a completely separate note, I am remembering a fanfic that seemed to get several things about the Premiere right, and I can't figure out why. It had the scene where Sarah throws the phone into the pool and the scene where he knocks out the guitarist (specifically mentioning how the guitarist is actually an assassin, who then attacks Chuck and wins because Chuck doesn't do a Kung Fu, flash).

Now, back to the story, where were we? Ah, right…

_Everyone spun around to look at Chuck's bedroom door, Sarah and Casey drew their guns. Ellie just smiled._

"_Sorry, I used the Morgan Door. You rang, Ellie?"_

_Jill Roberts had arrived._

Ellie looked around at everyone and groaned.

"Sarah, John, put those things away, I will not have you drawing guns in my house! Now stand down and stop interfering, this is between Jill and me." Ellie walked over to Jill and started giving her a hug, "Jill, it's so go to see you again."

She didn't get any farther than that because Jill was mad at her, very mad. As soon as she was in range, Jill kneed Ellie in the groin, spun 90 degrees and launched a side kick into Ellie's stomach, followed by a spin kick to her head. After Ellie went down, Jill kicked her in the stomach twice more for good measure.

Anna laughed, she was expecting this. Chuck was just shocked at someone beating up his sister. Sarah and Casey brought their guns up again, only to be stopped by Ellie's groan.

"Ulghh, what did I say about those guns?" Ellie then turned her head to Jill, "Feel better?"

"Much." Jill then offered her hand to help her up, which Ellie took, before continuing, "You've gotten soft, ma'am."

"No, I just figured that you would do something like that and I let you. I probably deserve it too."

Now Chuck was a little confused, "Uh, what?"

Casey grunted, "Moron, spies don't take time to talk about their lady feelings. They just simply fight it out."

"True, John, even lady spies do that on occasion. Oh and what did I say about the word 'Moron'?"

Casey growled. But, before he could respond Jill cut him off.

"So will someone fill me in?"

"Clearly Fulcrum is not dead, I have no idea what happened after I left, oh and Chuck here is the new Intersect; John and Sarah are his handlers."

"Well, what happened after you left is a very interesting story. However, right now, I've been on the run for the past 10 days with no hygienic facilities what so ever. So, would you mind if I take a shower before we start?"

"No, of course not, Jill."

"Good." Jill leaned in and whispered something to Ellie before she walked into the master bedroom and shut the door. Ellie turned back to everyone else, "Anna, I need you to draft us a new cover for Chuck and Morgan, I'm sorry, but if you're staying, he can't go to Hawaii."

"Maybe I should just let him go," Anna hesitantly asked, she didn't want to lose Morgan, yet she didn't want to drag Morgan down, away from his dreams.

"He won't go without you, Anna."

"I'll get right on it."

Ellie nodded and turned to Sarah and Casey, "You two need to get back to Castle," she wrote a quick message on some paper, "Get these people here ASAP."

They nodded and left, leaving Ellie and Chuck alone in her living room.

"Sit down, Chuck. We need to talk." Chuck sat.

Ellie took a deep breath, "You're angry I take it."

"Oh, yes, I'm angry, I'm feel betrayed. Here, I've done everything in my power for the past two years to keep you safe and it turns out that you have more experience than I do."

"Chuck I didn't tell you—"

"In order to keep me safe, same reason I didn't tell you about The Intersect. Why did you kick me out of Stanford though?"

"You were about to be pulled into the spy world from two directions. Project Omaha, the CIA recruitment program that brought me Bryce Larkin was looking at you. If they did indeed get your information then there would be nothing I could do. Also Fulcrum was showing a lot of interest in you. The fact that they approved of your relationship with Jill set off a lot of red flags. I didn't know why they wanted you. They could have wanted to recruit you, kill you, or use you to get to me. So, I did the only thing I could have, I ordered Bryce to use any means necessary to get away from Stanford. I had intended to pull some strings and get you your degree after the whole thing got blown over, but I had to leave and I also underestimated the effect Jill would have on you."

"What about Jill, clearly you kept in contact with her after she broke up with me?"

"Jill took the breakup almost as hard as you did. What the two of you had was as close to real as it could get in the spy world. I placed her in Stanford with the orders to live her life until Fulcrum came calling, through her Uncle Bernie. She broke it off with you because Fulcrum ordered her to. She tried to do everything she could to not do it. But, she didn't have a choice; if she refused Fulcrum would kill her and you. We both had hoped that you would move out quickly after she told you she was with Bryce. Clearly that plan backfired. Afterward, she threw herself into her work, I think on some level she felt that the faster she destroyed Fulcrum, the faster you two could maybe get back together. Alas, something happened, what I don't know yet."

"Ellie, are you sure that she can be trusted? I mean she did try to kill me and Sarah a few months ago."

"What happened to me wasn't so much getting my cover blown as having someone inside Counterweight try to kill me. Whoever did this would have had to not only know where I was that day, but actually been there. I can only account for the location of three people that day myself, Anna, who was with me, and Jill, who I can verify as being thousands of miles away at her graduation."

At this point, Jill came out, looking a lot better, "Okay, so are you ready to find out what happened?"

AN: Please review, thanks to those who have

AN2: This is the listing I have developed so far for Operation Counterweight

Langston Graham: Director of the Central Intelligence Agency

Ellie Bartowski: Director of Operation Counterweight, codename "Rose Thorn"

Bryce Larkin: CIA Agent

Jill Roberts: Operation Counterweight mole inside Fulcurm, Codenames:"Seashore" (CIA) and "Sandstorm" (Fulcurm)

Alex Forrest: CIA Agent

Anna Wu: CIA Agent, formerly of the Republic of China (Taiwan)'s National Security Bureau, Codename: "Lilly Dao"

As of yet unidentified female spy that Chuck has already met

As of yet unidentified male spy that Chuck has already met

Another as of yet unidentified male spy that Chuck has already met


	5. A Ring of Traitors

Disclaimer: I do not own the rights to the _Chuck_ TV series or characters. I do, however, reserve the rights for any characters I develop and the plot of this story.

Chuck vs. the Rose Thorn

By Jojobevco

Chapter 5

A Ring of Traitors

AN: The episode Chuck vs. First Class actually restored my faith in the series a little and made me hate Shaw just a bit less. Also, I like the new Hannah character. I feel she would serve as a good back up if things with Sarah fall through, which, through past experience with the show, they probably will. (Seriously we've had enough of this angst, get them together and lets have some relationship angst instead.)

After a quick drive from Casa Bartowski to Castle, Anna, Chuck, Ellie, Sarah and Casey were gathered around waiting to hear Jill's report. Before Jill started, Ellie turned to Sarah, "did you find the Agents I asked you to?"

"Yes, well sort of, the first one on your list said that he'd be out here as soon as he found a flight with a beautiful flight attendant on it."

"So that means tomorrow, knowing him."

"Probably, the other agent is currently on CIA deep cover assignment."

"Can they pull her?"

"No, she's in too deep, earliest they could get her out is in five months."

"Damn, I need her."

Jill cleared her throat and began, "Thanks to the damage that Operation Counterweight had caused, Fulcrum was dying, fast. There is no doubt of that. They were weeks away from collapsing. That was until, Ellie and Anna got in trouble. Elle tell us exactly what happened that day."

_Flashback_

_ Ellie and Anna walked down to the docks along the Thames in London. They were here to meet an arms merchant, one that had a connection to Fulcrum. They believed he was in possession of a nuclear warhead. They were here to take it off his hands, probably by taking him out. Elle and Anna entered the building and went through the usual frisking/boob groping by the thugs, and were escorted to their meeting with the boss upstairs. _

_ Ellie started by asking, "Do you have the device?"_

_ The arms dealer waved them over to a box with Russian printed on the side. He opened it and they all looked down at a very nice nuclear warhead._

_ Just as Ellie started verifying that the device worked the arms dealer got a call. Ellie ignored it while she was verifying the authenticity of the device. Anna, however, noticed the furtive glances the arms dealer was giving Ellie and discreetly moved over to the wall where a bunch of knives were. Anna grabbed one. The dealer hung up and turned to Ellie._

_ "Well, it is an honor, Rose Thorn and Lilly Dao. I'm a bit flattered that the CIA would send you after me."_

_ Anna was nonplussed, "How did you know?"_

_ "Simple, one of your own team sold you out."_

_ Ellie had looked up from the device and started moving toward a wall of weapons, "Really, who?"_

_ "Actually it was—"_

_ At this point he was finding it a bit hard to talk because of the knife sticking out of his throat_

_ "Damn it, Anna, I wanted to know who betrayed us."_

_ "We had the element of surprise, we'll investigate this later." Ellie and Anna disarmed the two grunts in the room and killed them with their own guns. They ran through the door and shot the rest of the guards as they were trying to get up from their card game._

_ After running a couple of blocks back into the city proper, they decided that it was safe. They doubled over, catching their breath._

_ "We need a plan," Anna wheezed._

_ "We've been blown. We need to leave, forever. Stay here in London. I'm going to go back to Langley and purge our records. We're leaving the CIA."_

_ "I have no place else to go."_

_ "Yes, you do. You're coming with me. I'll be back for you"_

_End Flashback_

"I flew back to Langley, purged my records and finished stuff up. Then, I flew back to London and Anna and killed Rose Thorn. I became Ellie Bartowski again, we got on a plane to LA where I met Devon, and the rest is history."

Jill continued her story, "within a week of you two leaving Graham had shut down Counterweight, ostensibly because we were no longer effective due to the traitor within our ranks. He would have been the one to purge Counterweight's files. Using Fulcrum's resources, under the guise of investigating the attack in London, I traced the call to the arms dealer's cell. It lead to one of our phones, specifically the one assigned to Alex Forrest."

"Forrest works for Fulcrum?" Elle, suffice it to say, was not surprised by this, she always hated Forrest, now she simply had an excuse to kill her.

"Not exactly, Fulcrum had no record of her, no code names, nothing. So, I looked through her phone records, trying to see why she would do this. I found her reason to blow your cover; two minutes before she called you she got a seven second phone call from another CIA cell phone."

"Who's was it?"

"The phone was assigned to Director Langston Graham."

This bomb shell had a few different reactions within the group. Sarah was shocked, Ellie and Anna were nodding as though it made sense, but they looked like they wanted to shoot someone, Casey was smirking, and Chuck was confused.

Sarah exploded, "I'm sorry, Roberts, but did you just say that the former _Director _of the Central Intelligence Agency was Fulcrum?"

"No, I didn't. Two weeks after Ellie and Anna left, Fulcrum was subject to the espionage version of a corporate takeover. Fulcrum was 'bought out,' if you'll keep with the analogy, by an organization known as 'The Ring.'"

"We know that Fulcrum is part of The Ring," Chuck pointed out. Bryce's dying words were burned into his memory.

"Fulcrum only became part of The Ring because it was dying. The damage that Counterweight had given it was just short of a death blow. I believe that The Ring ordered Graham to destroy Fulcrum, a competitor for world domination, just enough so that they could take it over. Forrest, who works for the Ring was ordered to halt your progress when the damage was sufficient enough to allow for a takeover."

"Do you have any proof of this?" Sarah asked.

"Well for starters, contrary to popular belief, Langston Graham is alive."

AN: Please Review! Thanks to those who have.


	6. The Traitor, the Jerk, the Mole, and the

Disclaimer: I do not own the rights to the _Chuck_ TV series or characters. I do, however, reserve the rights for any characters I develop and the plot of this story.

Chuck vs. the Rose Thorn

By Jojobevco

Chapter 6

The Traitor, the Jerk, the Mole, and the Husband

AN: Well, Nacho Sampler and Mask were ok, I guess, I liked the fact that Hannah and Chuck got together. In my opinion Hannah was good for Chuck. I agreed with putting Manoosh away, he wanted to sell the Intersect, and was therefore NOT Chuck.

Fake Name was a new low for me, Sarah and Shaw getting together was horrible, Chuck's not flashing, and his breaking up with Hannah for close to the same reasons that Sarah broke up with him were also not good. I liked Hannah, I felt that she would have been a good girlfriend for Chuck, and she didn't turn out to be a bad guy (yet!)

Beard is the best episode I've seen in a long time, perhaps since the Prague incident, first of all, this episode was all Chuck and made Shaw look like an idiot, the scene with Morgan was excellent, and the slow march back toward Chuck and Sarah being together begins. Oh and did anyone else notice that Doctors without Borders line?

In other news I just heard that Anna Wu (played by Julia Ling) will be returning at the end of the Season, here's hoping that she's not a member of the Ring.

_"Well for starters, contrary to popular belief, Langston Graham is alive."_

Uproar. That was the single word that could describe it; everyone had seen the footage from the Intersect Room Bombing, everyone _knew_ that he was dead.

"How can he be alive? We all saw him die, Roberts."

"Okay, ladies and gentlemen, how many other times have we seen someone die in this business only to have them reappear later? Biggest example Bryce Larkin blew up an Intersect Room, and was thought to be shot dead by our own John Casey. In Graham's case, a body was recovered, a body with traces that matched Graham's DNA profile. Except that the traces were planted on a body burned beyond recognition that matched his general appearance." Jill sighed and thought for a moment before snapping her fingers in a eureka moment. "Walker, access the surveillance footage for the Dulles Airport security checkpoint on September 30, 2008 at about 4:05 PM."

Sarah hoped on one of the computers, access the footage and put it up on the main screen. It went on for a few seconds before Jill suddenly shouted and pointed, "There, stop, magnify that section and enhance."

Sarah did. Everyone looked at the face of Langston Graham, clear as day, going through security. Jill popped in a flash drive and pulled up some images of tickets and another video.

"Graham got on a plane to LAX, booking first class actually. Graham chose this flight well; there were no congressmen, aids, government workers, CIA agents or anyone else that could identify him. When he landed he went to Fulcrum recruiting facility we went to last year. It happened to be the executive offices of Fulcrum at the time."

Sarah finally conceded the point, "Okay, so Graham is alive and working for the Ring."

Anna interjected, "The Ring is real? I thought that they were the spy world version of a scary bedtime story."

Ellie chuckled, "Oh, yes, the Ring is definitely real, at a time I thought they were connected to Fulcrum. That was one particular part of Counterweight I wanted to forget."

Casey grunted, "Sound like there's a story there, Ellie."

"I had to work with the head of the Counter-Ring investigation; he was an absolute jerk, he was the kind of person that thought he was the best thing since sliced bread, that he was infallible, and that he could do no wrong. Also, I had a source on the inside, a girl. She was one of the, um, more interesting people, I worked with. I never knew her name, not even a codename; she was simply 'The Source' and I was simply 'The Handler'."

"What happened to her?"

"She stopped sending me intel about three months before I left. The stop of her transmissions coincided with the death of a Ring Operative that matched her description. To the best of my knowledge, she's dead. It's funny, you know, I was always looking for a link between The Ring and Fulcrum, it turns out _we_ were the link."

Ellie took several minutes to collect herself before starting to speak again, "Okay, this is what we are going to do. Sarah and Jill, stay here and brief Beckman, watch her carefully while doing so. I'd rather like to think she's not Fulcrum or Ring, but for all we know, she could be. John, get a capture/sanction notice out on Forrest immediately, preferably capture. We will take no action on Graham, at least until we hear from Beckman. Anna, you're responsible for coming up with a new cover for Chuck and Morgan, preferably something with a bit more freedom than here. The cover also has to be good enough to keep Morgan from leaving to become a damn Benihana Chef. If he really wanted to know how to do it, Sarah, you, or I could teach him."

Chuck was confused, "uh, what?"

Ellie groaned, walked into the armory and came out with a knife, she did a few motions with it, eventually cutting a donut on the table, "Anna, Sarah, recognize that?"

"Yeah, that's straight out of the CIA's Knife Training Manual."

"Yes, it also corresponds with the Benihana Hibachi Training program. Anyway where was I, ah yes, Chuck and I will be going home to tell Devon."

"Tell Devon what?"

"Chuck, we're going to tell him that I'm a spy, he already knows that you are so it shouldn't be that much of a shock, besides, he deserves to know, and it's not fair to keep him in the dark about this." Ellie jerked her head toward Chuck and they headed up through the Orange Orange exit, while Anna walked over into the office to start developing a new cover for them. Casey gleefully went over to one of the computers to issue a Capture/Sanction on Forrest. Meanwhile, Sarah and Jill were about to brief the General.

"Alright, Agent Walker, clearly you have a problem with me. Let's clear the air now."

"Yes, I have a problem with you, namely with you almost shooting me. Chuck told me what happened at the Buy More before your capture."

"Walker, the key word there is almost, I would not have shot you if you didn't aim your gun at me first. Being under for over seven years tends to create a shoot first, ask questions later mentality. Today, I've felt better than I have in years. I don't have to lie anymore, I don't have to play the bad guy anymore, I'm free."

Sarah was not convinced. This woman had lied, cheated and tricked her way through life for the past seven years, so she looked into her eyes, really looked, and there she saw truth, she saw the hurt, the happiness, everything. She believed Jill.

"Alright, fine, but if I get even a suspicion that you're lying, I'll kill you myself."

Jill nodded, she could live with that, she had to.

Meanwhile, back at Casa Bartowski, Chuck and Ellie were about to tell Devon the truth. Devon walked in after a long day at the hospital, Chuck and Ellie motioned for him to sit down.

"Devon, we have something we need to tell you. Remember how Chuck told you he was a spy about a month ago?"

Devon worried, "Chuck, I swear, I didn't tell her, I'm sorry, bro, I didn't want her to find out."

"Devon, stop worrying, I didn't find out because of you, I found out on my own. The point of this conversation though is that I'm a spy for the CIA also. From 2001 to 2005 I was one of their best agents, I retired in 2005 for reasons that, for your own safety, I can't tell you. That was when we reconnected, on that flight back to LAX. After finding out what happened to Chuck I had to help him. Devon, I'll be honest with you, if his didn't happen then I probably wouldn't have told you, ever." By this time Ellie knew what she had to do, she had to give Devon a choice. "I completely understand if you want to divorce me Devon, and I wouldn't blame you if you did. It's probably better that you did, that way you'd be safe." Ellie bowed her head and waited for him to do something, in her heart she didn't want to let Devon go but she knew it was best for him.  
Devon got down on his knees in front of her and slowly pulled her chin up to look into her eyes. "Babe, listen to me, I promised to marry you for better or worse. While I don't appreciate that you kept a big secret like this from me, I understand why you did. Besides, the fact that my wife is a spy is totally awesome."

Ellie started crying and laughing at the same time. For all the ups and downs of this day, it ended on a very good note. Of course, tomorrow would be a busy day and most of Ellie's busy days ended up being bad days.

AN: Please review, thanks to those who have

AN2: Here is a running tally of the spies assigned to Operation Counterweight

Ellie Bartowski: Director of Operation Counterweight, codenames "Rose Thorn" (CIA), and "The Handler" (CIA Special Operation)

Bryce Larkin: CIA Agent, deceased

Jill Roberts: Operation Counterweight mole inside Fulcrum, Codenames:"Seashore" (CIA) and "Sandstorm" (Fulcrum)

Alex Forrest: Ring Mole inside Operation Counterweight (Currently a CIA Agent) Currently under a Capture/Sanction notice.

Anna Wu: CIA Agent, formerly of the Republic of China (Taiwan)'s National Security Bureau, Codename: "Lilly Dao"

Unnamed Female CIA Agent, currently on long term, deep cover assignment

Unnamed Male CIA Agent, currently en route to Burbank

Unnamed Female Operation Counterweight mole inside The Ring, Codename: "The Source" (CIA Special Operation), presumed deceased


	7. Making a Bit of Progress

Disclaimer: I do not own the rights to the _Chuck_ TV series or characters. I do, however, reserve the rights for any characters I develop and the plot of this story.

Chuck vs. the Rose Thorn

By Jojobevco

Chapter 7

Making a Bit of Progress

AN: Tic Tac was a very good episode, of course the first reaction I had was "Casey has a daughter?" But, I wish that they had done something a bit better with it, you know, the whole Casey has a daughter thing would have made for a good subplot to continue later (I hope they do)

Final Exam was just simply painful to watch, especially the ending, I mean come on, seriously, to pull an overused quote, "I find Sarah's lack of faith disturbing." Although, I get the sense we haven't seen the last of her red test. (For the record I wrote that line before American Hero aired)

American Hero, was good, it was the show that started redeeming the show, it answered questions, oh and good use of Shaw there.

Other Guy, can be summed up with a "Ding, Dong the Wicked Witch is Dead!" and "Finally, they fixed the damn show!"

The rest of the season was just great, except for the Stephen Bartowski dying part and the whole Ellie being manipulated by the Ring.

Everyone was tired the next morning, everyone in Castle was holding a mug of coffee and appearing especially bleary-eyed. Ellie turned to the group, "Okay, people, where are you on your assignments? John?"

Casey was smirking, "Agent Alex Forrest was picked up in the lobby of the CIA this morning; she had no idea whatsoever that a capture order had been issued. However, I'm told that the video itself is rather funny, they're going to be forwarding it to us later today."

Anna smiled, "Good, I'm bringing the popcorn." She, like a lot of the members of Counterweight, did not like Forrest, and not just for betraying them, but also because she's a "stuck up bitch."

"What else do we have?"

"Well, you have me."

Everyone turned and looked up at the Castle entrance, to a variety of reactions, Casey grunted, Sarah quirked an eyebrow, Chuck smiled, Jill groaned, and Ellie just looked at the new arrival in a daze.

Anna rolled her eyes and muttered, "Cue the cliché spy music."

Elle made a rather valiant effort to overcome her surprise and schooled her face back into a mask of relative normalcy, "Um, Roan, it's, uh good to see you again."

CIA Agent Roan Montgomery, just smiled and took a sip of his martini before walking down the stairs adjusting his immaculately kept jacket, he reached Ellie and kissed her on the hand.

"Eleanor, it is very good to see you again. I must say that I missed working with you."

"Yes, yes," suddenly Ellie snapped out of the daze she was in, "Roan, may I remind you that I am now a _very_ happily married woman?"

After Chuck heard that he started giving off a look halfway between gob smacked and nauseous, "Wait, wait a second here; Ellie and Roan were together? You have got to be kidding me." When no one bothered to correct him, Chuck got a disgusted look on his face, "Excuse me; I have to go throw up now."

Anna laughed, "Oh, stop being such a prude Chuck, your sister was quite the wild thing back in the day and based on what's been happening around here lately, I get the feeling that this isn't the last time this is going to happen."

Ellie's face suddenly became serious, "Anna, how about you give your report."

Anna swallowed, she probably shouldn't have said that, "Yes, Ma'am." She hit a button on the control and a business profile came up, "Everyone, meet Bargrim Technologies, the latest and greatest software development firm, featuring Charles Bartowski as its CEO and Morgan Grimes as its VP of Development. Also featuring Sarah Walker as its VP of Finance, John Casey as its VP of Security, Roan Montomery as its VP of Sales and yours truly as its Head of IT/Administrative assistant."

Elle pouted, just a bit, "What about me?"

"Well, you're still Doctor Ellie Woodcomb."

"You do realize that that will considerably limit my operational abilities."

"Well Doctor isn't exactly a cover you can get out of easily."

"I'll quit."

"And do what, Ellie, a doctor is always a doctor, they aren't exactly interchangeable like your average sales people or executive covers."

"I could transfer to another hospital, a CIA hospital, and operate out of there."

Jill snorted, "Really? What a _spectacular_ idea! And what happens when Rose Thorn get's recognized by someone? You made a lot of enemies throughout the years, many of whom still work for the CIA."

Ellie sighed, "We'll think about it later," she turned to Sarah and Jill, "Okay, so what's your analysis of your conversation with the General last night?"

Jill glared at Sarah out of the corner of her life, "_We_ came to the conclusion that she was not aware that Graham was alive. We also tested the conversation under a voice stress analyzer and tracking micro-expressions against key words and phrases. To the best of our knowledge she is not a member of Fulcrum or the Ring."

"Good. That's someone that we only have to keep one eye on."

Chuck was, in all his naivety, confused, "What, but I thought we just determined that she wasn't Fulcrum?"

"We did, Chuck, but do you seriously think I'm going to believe any analysis that says someone isn't Fulcrum? I only trust the people in this room, Chuck, and a _very_ select few outside of it. I've had at most a total of five minutes of conversation with Beckman and while I trust Jill's judgment, it takes years of interaction and life threatening experiences and missed opportunities of betrayal for me to completely trust someone."

Chuck looked a bit more confused, "I thought the point of the spy world was that people never trusted anyone?"

"Chuck, you have to draw the line of trust somewhere. If you never trusted anyone than you'd be a paranoid idiot always looking over your shoulder." She glared at Casey here, who just shrugged.

"Hey, it's how I keep my sanity."

"Whatever makes you happy, John. So, we've dealt with Beckman, our new covers, and now that Roan is here, what's left?"

Everyone looked at Chuck.

"What?"

"Now would be a good time to start your training, Chuck. John, take him to the firing range and get him started on the basics. Roan, go buy a penthouse, and I mean the apartment, not the magazine."

The man in question scoffed, "Roan Montgomery never needs a magazine."

Ellie, rolled her eyes and blushed, "As I'm all too aware. Jill, start going through the records of the assault on Castle and the Intersect Facility, last week, see if you can pick up anything."

Jill nodded and moved to one of the computers.

"Anna, start working on Morgan."

"I'd love to." Anna started skipping up the stairs before Ellie stopped her.

"You _know _what I mean, Agent Wu."

Anna nodded, "Yes, ma'am."

"Okay then, break!"

Everyone left, leaving Sarah and Ellie alone in the Castle control room. Sarah stood, looking at Ellie.

"You're wondering why I didn't say I trusted your judgment."

"It had crossed my mind."

"First of all, I don't know you, professionally, I mean. Personally, you're one of my closest friends. The second is Langston Graham."

"What?"

"After seeing your reaction to his treason last night I looked at your file, to find the connection."

"Your connection is similar."

"Yes, but unlike you, I had already accepted the possibility that he could have betrayed me. It actually made sense."

Sarah sighed, as much as she didn't want to admit it, Ellie was right, "So now what do we do?"

"We train, Sarah, it's been years since I've had to take someone out." They both walked back into the dojo like room. Ellie grabbed a bo and tossed it to Sarah.

"Ready?"

"Always."

They briefly bowed before starting to swing their staffs.

AN: Please Review! Thanks to those who have.

AN2: The next chapter will probably skip ahead to the events of "Chuck versus the Pink Slip"


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